I wanted to calculate the RMSD of overall protein and RMSF per residues. I have several proteins downloaded from the PDB (not snapshots of MD simulation). Can any one suggest me the scripts for both? I know there is option in AMBER and other MD simulation programme. But if some one share me the script to calculate the RMSD and RMSF, it will be highly useful for my studies. I am beginner in the coding.
Thank you
Script to calculate RMSD and RMSF using AMBER
cpptraj -i input_file
where your input file contains:
parm topolgy_file
trajin coordinate_file
rms first mass out rmsd_output.dat
atomicfluct out rmsf_output.dat :residue_no byres
#residue_no is the residues for which you want to calculate RMSF
See the amber manual for more detail description.
If you want to compare structural differences between different proteins from PDB, I guess what you want to do is instead aligning them e.g. in PyMOL and get the RMSD value from there, because the feature to calculate RMSD in AMBER is only for comparing same structures over time (atom name and number should match).
Furthermore, you can not even calculate RMSF because this term is meant to calculate differences between same structures over simulation time, which is not in your case
Dear Pritam, Supriyo and Eko thanks for adding your answers. I don't think we can use Chimera MatchMaker tool for calculating RMSD per residue. As Eko suggested if we are downloading the proteins directly from PDB, it may have different atom numbers. So AMBER won't work it seems.
I will repeat my question again. If I need to compute the residue wise fluctuation for the same class of protein downloading from PDB what I have to do?
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